This study aimed to determine the effect of 10 and 15% concentrations of Azadirachta indica oil (v/v) and Tithonia diversifolia and Thevetia peruviana liquid manure (w/v) on some key characteristics of tomato fruits. For this purpose, the extracts were sprayed on the tomato plants every two weeks until the fruits were harvested. The results show that the 15% T. diversifolia mash had the most significant positive impact (p < 0.05) on the size, weight, and ability of tomato fruits to protect DNA from denaturation. Indeed, compared to fruits harvested from untreated plants, this treatment increased the surface area by 75.38%, the weight by 72.74%, and the protective capacity of fruits against hydrogen peroxide-induced DNA denaturation by 82.96%. On the other hand, the highest lycopene content was obtained with A. indica at 10% (139.13 ± 4.35 μg/g MF), and that of phenols was observed with T. peruviana at 10% (31.07 ± 1.06 mg eq catechin/g MF). Also, there is a positive and significant correlation (p < 0.05) between phenol content and DPPH (2.2-diphenyl-1-picrylhydrazyl) and FRAP (ferric reducing antioxidant power) free radical scavenging activities of tomato fruits. Thus, this study shows that wild plant extracts are able to improve fruit quality.